Open Access

Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for ependymoma using integrated bioinformatics analysis

  • Authors:
    • Biao Yang
    • Jun‑Xi Dai
    • Yuan‑Bo Pan
    • Yan‑Bin Ma
    • Sheng‑Hua Chu
  • View Affiliations

  • Published online on: September 30, 2019     https://doi.org/10.3892/ol.2019.10941
  • Pages: 6079-6089
  • Copyright: © Yang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Ependymomas (EPNs) are one of the most common types of malignant neuroepithelial tumors. In an effort to identify potential biomarkers involved in the pathogenesis of EPN, the mRNA expression profiles of the GSE25604, GSE50161, GSE66354, GSE74195 and GSE86574 datasets, in addition to the microRNA (miRNA/miR) expression profiles of GSE42657 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) between EPN and normal brain tissue samples were identified using the Limma package in R and GEO2R, respectively. Functional and pathway enrichment analyses were conducted using the Database for Annotation, Visualization and Integrated Discovery. A protein‑protein interaction network was constructed using the Search Tool for Retrieval of Interacting Genes database, which was visualized using Cytoscape. The targeted genes of DEMs were predicted using miRWalk2.0 and a miRNA‑mRNA regulatory network was constructed. Following analysis, a total of 948 DEGs and 129 DEMs were identified. Functional enrichment analysis revealed that 609 upregulated DEGs were significantly enriched in ‘PI3K‑Akt signaling pathway’, while 339 downregulated DEGs were primarily involved in ‘cell junction’ and ‘retrograde endocannabinoid signaling’. In addition, 6 hub genes [cyclin dependent kinase 1, CD44 molecule (Indian blood group) (CD44), proliferating cell nuclear antigen (PCNA), MYC, synaptotagmin 1 (SYT1) and kinesin family member 4A] and 6 crucial miRNAs [homo sapiens (hsa)‑miR‑34a‑5p, hsa‑miR‑449a, hsa‑miR‑106a‑5p, hsa‑miR‑124‑3p, hsa‑miR‑128‑3p and hsa‑miR‑330‑3p] were identified as biomarkers and potential therapeutic targets for EPN. Furthermore, a microRNA‑mRNA regulatory network was constructed to highlight the interactions between DEMs and their target DEGs; this included the hsa‑miR‑449a‑SYT1, hsa‑miR‑34a‑5p‑SYT1, hsa‑miR‑330‑3p‑CD44 and hsa‑miR‑124‑3p‑PCNA pairs, whose expression levels were confirmed using reverse transcription‑quantitative polymerase chain reaction. In conclusion, the present study may provide important data for the investigation of the molecular mechanisms of EPN pathogenesis.
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December-2019
Volume 18 Issue 6

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Spandidos Publications style
Yang B, Dai JX, Pan YB, Ma YB and Chu SH: Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for ependymoma using integrated bioinformatics analysis. Oncol Lett 18: 6079-6089, 2019
APA
Yang, B., Dai, J., Pan, Y., Ma, Y., & Chu, S. (2019). Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for ependymoma using integrated bioinformatics analysis. Oncology Letters, 18, 6079-6089. https://doi.org/10.3892/ol.2019.10941
MLA
Yang, B., Dai, J., Pan, Y., Ma, Y., Chu, S."Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for ependymoma using integrated bioinformatics analysis". Oncology Letters 18.6 (2019): 6079-6089.
Chicago
Yang, B., Dai, J., Pan, Y., Ma, Y., Chu, S."Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for ependymoma using integrated bioinformatics analysis". Oncology Letters 18, no. 6 (2019): 6079-6089. https://doi.org/10.3892/ol.2019.10941